The Son of the Chicken, being a three-headed bird whose heads have different expressions, bears a resemblance to the Pokemon Dodrio.
This isn't the first time Pokemon has been indirectly referenced on the show. One of Courage's transformations in "A Night at the Katz Motel" resembles Dragonite. Pokemon was a popular show on Cartoon Network, airing on its Toonami block, so it's a possibility Michelle Dilworth was influenced by Dodrio when she came up with the way the chicken's son looked.
The Son could also be a reference to fellow Cartoon Cartoon Ed, Edd, 'n' Eddy.
During the scene where Courage is being chased by the egg bomb, the Lone Ranger's theme is played in the background (it is really called "Finale" from the "William Tell Overture," composed by "Gioachino Rossini").
The engine on the train is a 2-8-0 engine or an American Consolidation type steam locomotive. Locomotives of this wheel arrangement were used most common on American railroads during the 1800s and 1830s and were given the name "American" because of all of the work they did on every railroad until 1928. These types of engines have ten wheels (two leading wheels, four drive wheels, and no trailing wheels).
A laser beam melts the lower half of Eustace into a puddle of ooze, yet later he is shown slithering along on his liquefied lower body (this may be an example of cartoon physics).